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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ), 'gf_id' => 'HOM05D001210', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001210' ), 'data_identifier' => 'HOM05D001210', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001210', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30010' => 'bna', 'A03p09230' => 'bna', 'A07p10620' => 'bna', 'A08p25010' => 'bna', 'A09p22380' => 'bna', 'A09p36840' => 'bna', 'A10p20710' => 'bna', 'Aa31LG11G10760' => 'aar', 'Aa31LG1G20310' => 'aar', 'Aa31LG6G6080' => 'aar', 'Aa31LG9G6400' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1375' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.796' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.872' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.873' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.270' => 'aag', 'Actinidia00077' => 'ach', 'Actinidia11380' => 'ach', 'Actinidia16748' => 'ach', 'Actinidia19484' => 'ach', 'Actinidia39938' => 'ach', 'Ah.09g232950' => 'amhyb', 'Ah.14g086760' => 'amhyb', 'Ah.16g102000' => 'amhyb', 'AL1G14240' => 'aly', 'AL1G43360' => 'aly', 'AL6G30320' => 'aly', 'AL8G11890' => 'aly', 'Aqoxy1G01871' => 'aox', 'Aqoxy2G03227' => 'aox', 'Aqoxy3G03928' => 'aox', 'Aqoxy5G00118' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0ZKW04' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3S85UN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BCBY10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K65USX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PFE7S7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YCEX9W' => 'arhy', 'AT1G04560' => 'ath', 'AT1G29520' => 'ath', 'AT5G18970' => 'ath', 'AT5G46530' => 'ath', 'ATR0626G296' => 'atr', 'ATR0626G315' => 'atr', 'ATR0686G080' => 'atr', 'ATR0787G034' => 'atr', 'Atru.chr10.1413' => 'acertr', 'Atru.chr4.1894' => 'acertr', 'Atru.chr4.2670' => 'acertr', 'AUR62008969' => 'cqu', 'AUR62011793' => 'cqu', 'AUR62014534' => 'cqu', 'AUR62024640' => 'cqu', 'AUR62027552' => 'cqu', 'AUR62027553' => 'cqu', 'AUR62035368' => 'cqu', 'AUR62035803' => 'cqu', 'AUR62035880' => 'cqu', 'BcaB01g04881' => 'bca', 'BcaB01g05285' => 'bca', 'BcaB03g12164' => 'bca', 'BcaB03g13485' => 'bca', 'BcaB03g13880' => 'bca', 'BcaB07g30833' => 'bca', 'BcaB07g32544' => 'bca', 'BcaB08g36631' => 'bca', 'BcaC01g00116' => 'bca', 'BcaC03g16859' => 'bca', 'BcaC04g18635' => 'bca', 'BcaC04g21701' => 'bca', 'BcaC05g26976' => 'bca', 'BcaC06g35437' => 'bca', 'BcaNung05972' => 'bca', 'BcaNung05973' => 'bca', 'BcaNung06559' => 'bca', 'BolC2t10793H' => 'bol', 'BolC3t13550H' => 'bol', 'BolC3t19848H' => 'bol', 'BolC5t29055H' => 'bol', 'BolC5t31554H' => 'bol', 'BolC7t42113H' => 'bol', 'BolC8t52746H' => 'bol', 'BolC9t55732H' => 'bol', 'BolC9t58622H' => 'bol', 'BraA02t08021Z' => 'bra', 'BraA07t28856Z' => 'bra', 'BraA08t34456Z' => 'bra', 'BraA09t37842Z' => 'bra', 'BraA09t39202Z' => 'bra', 'BraA09t42111Z' => 'bra', 'BraA10t42568Z' => 'bra', 'BraA10t44134Z' => 'bra', 'C02p47530' => 'bna', 'C03p10770' => 'bna', 'C03p75970' => 'bna', 'C05p02730' => 'bna', 'C05p28320' => 'bna', 'C07p16200' => 'bna', 'C09p28650' => 'bna', 'C09p57530' => 'bna', 'CAN.G257.54' => 'can', 'CAN.G305.31' => 'can', 'CAN.G358.139' => 'can', 'CAN.G522.9' => 'can', 'CAN.G812.25' => 'can', 'CANSAT35G1758' => 'cansat', 'CANSAT64G0839' => 'cansat', 'CANSAT78G0816' => 'cansat', 'CANSAT78G1850' => 'cansat', 'CARHR003910' => 'chi', 'CARHR028910' => 'chi', 'CARHR175050' => 'chi', 'CARHR194030' => 'chi', 'Carub.0001s0378' => 'cru', 'Carub.0001s2775' => 'cru', 'Carub.0006s1727' => 'cru', 'Carub.0008s0138' => 'cru', 'Ca_02568_v3' => 'car', 'Ca_10528_v3' => 'car', 'Ca_21581_v3' => 'car', 'Ca_25277_v3' => 'car', 'Cc03_g02930' => 'ccan', 'Cc03_g06550' => 'ccan', 'Cc07_g08960' => 'ccan', 'Cc09_g09750' => 'ccan', 'CDE02G1012' => 'cde', 'CDE02G1491' => 'cde', 'CDE02G1807' => 'cde', 'CDE08G1560' => 'cde', 'CDE09G1220' => 'cde', 'CDE09G1281' => 'cde', 'Cfa001035' => 'cfa', 'Cfa014804' => 'cfa', 'Cfa015554' => 'cfa', 'Ciclev10006007m.g' => 'ccl', 'Ciclev10006056m.g' => 'ccl', 'Ciclev10013040m.g' => 'ccl', 'Ciclev10017020m.g' => 'ccl', 'CiPaw.01G157800' => 'cil', 'CiPaw.01G176400' => 'cil', 'CiPaw.03G060100' => 'cil', 'CiPaw.10G096500' => 'cil', 'ClCG01G024190' => 'cla', 'ClCG03G007210' => 'cla', 'ClCG05G005530' => 'cla', 'ClCG06G007310' => 'cla', 'ClCG06G007320' => 'cla', 'COL.COLO4_15992' => 'col', 'COL.COLO4_16188' => 'col', 'COL.COLO4_21621' => 'col', 'COL.COLO4_22803' => 'col', 'Cpa.g.sc16.51' => 'cpa', 'Cpa.g.sc17.171' => 'cpa', 'Cpa.g.sc179.15' => 'cpa', 'Cpa.g.sc179.19' => 'cpa', 'Cpa.g.sc59.22' => 'cpa', 'CsaV3_1G032800' => 'csa', 'CsaV3_2G012350' => 'csa', 'CsaV3_3G013850' => 'csa', 'CsaV3_6G051340' => 'csa', 'CSS0020266' => 'camsi', 'CSS0020631' => 'camsi', 'CSS0040990' => 'camsi', 'CSS0041469' => 'camsi', 'DCAR_002424' => 'dca', 'DCAR_007912' => 'dca', 'DCAR_014903' => 'dca', 'DCAR_027141' => 'dca', 'DCAR_027358' => 'dca', 'DCAR_027957' => 'dca', 'Dinv03634' => 'din', 'Dinv27127' => 'din', 'Dinv32300' => 'din', 'Dinv38363' => 'din', 'Duzib151G0472' => 'dzi', 'Duzib192G0197' => 'dzi', 'Duzib212G0025' => 'dzi', 'Duzib212G0681' => 'dzi', 'Duzib235G0483' => 'dzi', 'ECA234G3459' => 'eca', 'ECA236G1009' => 'eca', 'ECA236G1677' => 'eca', 'ECA236G4652' => 'eca', 'ECA248G3912' => 'eca', 'EL10Ac2g04601' => 'bvu', 'EL10Ac3g06707' => 'bvu', 'EL10Ac8g18722' => 'bvu', 'EL10Ac8g19798' => 'bvu', 'EL10As5g23543' => 'bvu', 'Eucgr.D00344' => 'egr', 'Eucgr.H00118' => 'egr', 'Eucgr.H02898' => 'egr', 'Eucgr.H03634' => 'egr', 'FAN02G4104' => 'fan', 'FAN07G2259' => 'fan', 'FAN09G1197' => 'fan', 'FAN11G3795' => 'fan', 'FAN12G1751' => 'fan', 'FAN12G2863' => 'fan', 'FAN16G2155' => 'fan', 'FAN17G0172' => 'fan', 'FAN17G0637' => 'fan', 'FAN21G0182' => 'fan', 'FAN22G2166' => 'fan', 'FAN25G3772' => 'fan', 'FvH4_3g06430' => 'fve', 'FvH4_4g05050' => 'fve', 'FvH4_4g14182' => 'fve', 'FvH4_6g45320' => 'fve', 'Glyma.05G164300' => 'gma', 'Glyma.07G255100' => 'gma', 'Glyma.08G121700' => 'gma', 'Glyma.09G085600' => 'gma', 'Glyma.10G205900' => 'gma', 'Glyma.15G195600' => 'gma', 'Glyma.17G019200' => 'gma', 'Glyma.20G184600' => 'gma', 'Gohir.A05G151500' => 'ghi', 'Gohir.A06G135500' => 'ghi', 'Gohir.A09G200600' => 'ghi', 'Gohir.A09G230600' => 'ghi', 'Gohir.A10G106750' => 'ghi', 'Gohir.D05G153900' => 'ghi', 'Gohir.D06G140700' => 'ghi', 'Gohir.D09G194800' => 'ghi', 'Gohir.D09G231700' => 'ghi', 'Gohir.D10G147400' => 'ghi', 'Gohir.D10G160600' => 'ghi', 'Gorai.006G218200' => 'gra', 'Gorai.006G254400' => 'gra', 'Gorai.009G158200' => 'gra', 'Gorai.010G164200' => 'gra', 'Gorai.011G164500' => 'gra', 'Gorai.011G180300' => 'gra', 'GSVIVG01017867001' => 'vvi', 'GSVIVG01021373001' => 'vvi', 'GSVIVG01027944001' => 'vvi', 'GSVIVG01031072001' => 'vvi', 'HanXRQChr01g0002991' => 'han', 'HanXRQChr01g0023091' => 'han', 'HanXRQChr04g0114221' => 'han', 'HanXRQChr04g0114241' => 'han', 'HanXRQChr11g0342361' => 'han', 'HanXRQChr15g0465961' => 'han', 'HanXRQChr15g0468161' => 'han', 'HanXRQChr17g0564911' => 'han', 'Haze_05480' => 'cav', 'Haze_11485' => 'cav', 'Haze_14134' => 'cav', 'Hma1.2p1_0015F.1_g010410' => 'hma', 'Hma1.2p1_0136F.1_g062130' => 'hma', 'Hma1.2p1_2418F.1_g321800' => 'hma', 'HPP92_005110' => 'vpl', 'HPP92_007996' => 'vpl', 'HPP92_009788' => 'vpl', 'Hund02944' => 'sun', 'Hund16128' => 'sun', 'Hund20486' => 'sun', 'Hund21472' => 'sun', 'Hund21473' => 'sun', 'Hund21474' => 'sun', 'Hund21475' => 'sun', 'Lalb_Chr02g0151891' => 'lal', 'Lalb_Chr07g0186111' => 'lal', 'Lalb_Chr11g0073291' => 'lal', 'Lalb_Chr12g0196271' => 'lal', 'Lalb_Chr13g0304031' => 'lal', 'Lalb_Chr23g0275961' => 'lal', 'Lj1A1181T112' => 'lonja', 'Lj3A804T33' => 'lonja', 'Lj3C638G7' => 'lonja', 'Lj3C804T12' => 'lonja', 'Lj4g0023028' => 'lja', 'Lj4g0027082' => 'lja', 'Lj5g0023016' => 'lja', 'Lj6A637T66' => 'lonja', 'Lj6g0004720' => 'lja', 'Lsat_1_v5_gn_2_14620' => 'lsa', 'Lsat_1_v5_gn_2_79701' => 'lsa', 'Lsat_1_v5_gn_4_27540' => 'lsa', 'Lsat_1_v5_gn_6_68341' => 'lsa', 'Lsat_1_v5_gn_7_26060' => 'lsa', 'Lsat_1_v5_gn_8_110060' => 'lsa', 'Manes.02G067000' => 'mes', 'Manes.03G157000' => 'mes', 'Manes.07G121700' => 'mes', 'Manes.15G046800' => 'mes', 'Manes.15G116500' => 'mes', 'Manes.17G064500' => 'mes', 'Mapoly0022s0022' => 'mpo', 'Mapoly0022s0081' => 'mpo', 'Mapoly0022s0082' => 'mpo', 'Mapoly0022s0083' => 'mpo', 'Mapoly0044s0120' => 'mpo', 'Mapoly0052s0098' => 'mpo', 'MBI07_g08905_MAGBIO' => 'mbi', 'MBI07_g25504_MAGBIO' => 'mbi', 'MBI17_g29608_MAGBIO' => 'mbi', 'MD05G1292100' => 'mdo', 'MD09G1085800' => 'mdo', 'MD10G1267900' => 'mdo', 'MD13G1180300' => 'mdo', 'MD13G1224200' => 'mdo', 'MD16G1181200' => 'mdo', 'MD16G1229000' => 'mdo', 'MD17G1074700' => 'mdo', 'Medtr1g094035' => 'mtr', 'Medtr2g049340' => 'mtr', 'Medtr4g117600' => 'mtr', 'Medtr6g068860' => 'mtr', 'MELO3C002702.2' => 'cme', 'MELO3C006578.2' => 'cme', 'MELO3C007171.2' => 'cme', 'MELO3C023049.2' => 'cme', 'Migut.G00253' => 'egut', 'Migut.G00585' => 'egut', 'Migut.G00586' => 'egut', 'Migut.H00203' => 'egut', 'Migut.H01392' => 'egut', 'Migut.N00318' => 'egut', 'MSTRG.10022' => 'ama', 'MSTRG.14754' => 'ama', 'MSTRG.16200' => 'ama', 'Nitab4.5_0000745g0070' => 'nta', 'Nitab4.5_0000982g0110' => 'nta', 'Nitab4.5_0001041g0060' => 'nta', 'Nitab4.5_0001283g0040' => 'nta', 'Nitab4.5_0001769g0130' => 'nta', 'Nitab4.5_0001826g0020' => 'nta', 'Nitab4.5_0002288g0080' => 'nta', 'Nitab4.5_0003714g0050' => 'nta', 'Nitab4.5_0005951g0010' => 'nta', 'Nn1g02129' => 'nnu', 'Nn3g19812' => 'nnu', 'Nn3g20925' => 'nnu', 'Nn4g26154' => 'nnu', 'Nn6g34368' => 'nnu', 'Oeu001055.1' => 'oeu', 'Oeu020138.1' => 'oeu', 'Oeu035120.1' => 'oeu', 'Oeu037665.1' => 'oeu', 'Os01g0247900' => 'osa', 'Os01g0699900' => 'osa', 'Os02g0731500' => 'osa', 'Os05g0381400' => 'osa', 'Os07g0422100' => 'osa', 'Os10g0464300' => 'osa', 'Peaxi162Scf00095g00719' => 'pax', 'Peaxi162Scf00164g00311' => 'pax', 'Peaxi162Scf00531g00009' => 'pax', 'Peaxi162Scf00649g00011' => 'pax', 'Peaxi162Scf00653g00414' => 'pax', 'Peaxi162Scf01327g00130' => 'pax', 'PGR004G1264' => 'pgr', 'PGR031G2259' => 'pgr', 'PGR031G2597' => 'pgr', 'PGR065G0007' => 'pgr', 'PGSC0003DMG400001503' => 'stu', 'PGSC0003DMG400003075' => 'stu', 'PGSC0003DMG400004354' => 'stu', 'PGSC0003DMG400012676' => 'stu', 'PGSC0003DMG400037381' => 'stu', 'Phvul.002G244300' => 'pvu', 'Phvul.003G106300' => 'pvu', 'Phvul.007G100700' => 'pvu', 'Phvul.009G214500' => 'pvu', 'Potri.001G354500' => 'ptr', 'Potri.008G200000' => 'ptr', 'Potri.008G200300' => 'ptr', 'Potri.010G064200' => 'ptr', 'Potri.011G077800' => 'ptr', 'Potri.017G113000' => 'ptr', 'Pp3c11_14870' => 'ppa', 'Pp3c11_14880' => 'ppa', 'Pp3c12_25110' => 'ppa', 'Pp3c18_17550' => 'ppa', 'Pp3c1_14380' => 'ppa', 'Pp3c20_13220' => 'ppa', 'Pp3c2_25930' => 'ppa', 'Pp3c4_21960' => 'ppa', 'Pp3c4_30620' => 'ppa', 'Pp3c4_3440' => 'ppa', 'Pp3c4_3450' => 'ppa', 'Pp3c7_11540' => 'ppa', 'Prupe.1G050900' => 'ppe', 'Prupe.1G148600' => 'ppe', 'Prupe.4G073300' => 'ppe', 'Psat1g018160' => 'psa', 'Psat1g020400' => 'psa', 'Psat4g032560' => 'psa', 'Psat6g179120' => 'psa', 'PSO063G4599' => 'pso', 'PSO170G5217' => 'pso', 'PSO407G0378' => 'pso', 'PSO541G3832' => 'pso', 'PSO675G2263' => 'pso', 'PSO764G0200' => 'pso', 'PSO832G4598' => 'pso', 'QL02p051529' => 'qlo', 'QL05p060715' => 'qlo', 'QL06p005913' => 'qlo', 'QL06p005915' => 'qlo', 'QL06p021785' => 'qlo', 'RcHm_v2.0_Chr2g0163081' => 'rch', 'RcHm_v2.0_Chr4g0395971' => 'rch', 'RcHm_v2.0_Chr4g0419021' => 'rch', 'RcHm_v2.0_Chr5g0012871' => 'rch', 'Rhsim02G0018100' => 'rsi', 'Rhsim02G0047900' => 'rsi', 'Sabra08G0160900' => 'sbr', 'Sabra10G0042800' => 'sbr', 'Sabra11G0072400' => 'sbr', 'Sabra16G0233100' => 'sbr', 'SalBow2G0800' => 'sbo', 'SalBow2G3053' => 'sbo', 'SalBow3G1162' => 'sbo', 'SalBow3G1902' => 'sbo', 'SalBow3G4200' => 'sbo', 'SalBow7G1323' => 'sbo', 'SalBow8G3147' => 'sbo', 'Sc05g0006620' => 'sci', 'Sc13g0003060' => 'sci', 'Sc17g0005240' => 'sci', 'Sc17g0005250' => 'sci', 'Sc25g0004860' => 'sci', 'Sed0000681' => 'sed', 'Sed0002873' => 'sed', 'Sed0005164' => 'sed', 'Sed0020186' => 'sed', 'Sed0023151' => 'sed', 'Sed0025818' => 'sed', 'SEGI_03176' => 'sgi', 'SEGI_06629' => 'sgi', 'SEGI_06690' => 'sgi', 'SEGI_15952' => 'sgi', 'SEGI_20746' => 'sgi', 'SEGI_28456' => 'sgi', 'SEGI_28847' => 'sgi', 'SEGI_30967' => 'sgi', 'SEGI_33159' => 'sgi', 'SEGI_36413' => 'sgi', 'SEGI_37100' => 'sgi', 'SEGI_38093' => 'sgi', 'SEGI_40057' => 'sgi', 'SGA_v2.0_scaffold123G33462' => 'sas', 'SGA_v2.0_scaffold166G38391' => 'sas', 'SGA_v2.0_scaffold1G00130' => 'sas', 'SGA_v2.0_scaffold31G12621' => 'sas', 'SGA_v2.0_scaffold33G13476' => 'sas', 'SGA_v2.0_scaffold5G02557' => 'sas', 'SMO123G0001' => 'smo', 'SMO165G0134' => 'smo', 'SMO172G0064' => 'smo', 'SMO201G0110' => 'smo', 'SMO328G0033' => 'smo', 'SMO347G0407' => 'smo', 'SMO367G1181' => 'smo', 'Solyc01g080290.3' => 'sly', 'Solyc02g071310.3' => 'sly', 'Solyc02g085770.4' => 'sly', 'Solyc05g053160.3' => 'sly', 'Solyc09g090800.2' => 'sly', 'Sopen01g032080' => 'spe', 'Sopen02g020370' => 'spe', 'Sopen02g030460' => 'spe', 'Sopen05g031670' => 'spe', 'Sopen09g033750' => 'spe', 'Sp1g03400' => 'spa', 'Sp1g25460' => 'spa', 'Sp2g11360' => 'spa', 'Sp6g25420' => 'spa', 'TAR362G0536' => 'tar', 'TAR365G0190' => 'tar', 'TAR365G0443' => 'tar', 'TAR624G0228' => 'tar', 'TAR626G0597' => 'tar', 'TAR629G0915' => 'tar', 'TAR629G2793' => 'tar', 'THA.LOC104806110' => 'tha', 'THA.LOC104812652' => 'tha', 'THA.LOC104818786' => 'tha', 'THA.LOC104820623' => 'tha', 'THA.LOC104826101' => 'tha', 'Thecc.04G136900' => 'tca', 'Thecc.04G219000' => 'tca', 'Thecc.04G267900' => 'tca', 'Thecc.06G158100' => 'tca', 'Thhalv10001059m.g' => 'esa', 'Thhalv10008973m.g' => 'esa', 'Thhalv10009503m.g' => 'esa', 'Thhalv10014847m.g' => 'esa', 'TPR.G12501' => 'tpr', 'TPR.G18408' => 'tpr', 'TPR.G22002' => 'tpr', 'TPR.G9801' => 'tpr', 'TWI09G0191' => 'twi', 'TWI09G1130' => 'twi', 'TWI53G0726' => 'twi', 'TWI53G0814' => 'twi', 'TWI53G0981' => 'twi', 'TWI73G0074' => 'twi', 'TWI73G0837' => 'twi', 'TWI74G0790' => 'twi', 'unitig_37.g12108' => 'ugi', 'unitig_52.g17403' => 'ugi', 'vmacro15293' => 'vma', 'vmacro15488' => 'vma', 'vmacro18083' => 'vma', 'VMungo0251G2378' => 'vmu', 'VMungo0720G0979' => 'vmu', 'VMungo1215G2672' => 'vmu', 'VMungo1309G0370' => 'vmu', 'Zm00001eb140210' => 'zma', 'Zm00001eb155680' => 'zma', 'Zm00001eb306010' => 'zma', 'Zm00001eb346830' => 'zma', 'Zm00001eb360960' => 'zma' ) $gf_id = 'HOM05D001210' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001210' ) $data_identifier = 'HOM05D001210' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 4, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 13, 'sas' => (int) 6, 'smo' => (int) 7, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 8, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb360960' $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